Put the good fob into ignition and press to switch on ignition only but do not start the engine. With your manual key, lock the door. Now press the fob you are trying to train twice. It should take the code. Unlock the door, remove the good fob and test the newly trained fob.
Here is VW Passat B6 2005-2010 fuse box and relay panel location and diagram (explanation). For US customers can find Car Fuses Assortment Kit, Standard & Mi
I tend to agree with the air bubble thought too assuming 1.8. I've got 4 1.8 Passat B5.5's and a B6 A4 I support (Family) and I it takes a while to work the air out of them unless you have a means to pressurize them. The B6 is the easiest with the allen head screw on the top metal coolant pipe. You did Bleed the system using the top heater core
That module 56 readout would've given part number and what settings it's got. The pressing CD button twice should be done when you've got your Aux connected and playing. If it's just the single jack in the centre console then try giving it a squirt with Servisol as they're prone to dust. Otherwise make sure it's connected to your headunit by
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